Development of a Core Collection Based on EST-SSR Markers and Phenotypic Traits in Foxtail Millet [ Setaria italica (L.)
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J. Crop Sci. Biotech. 2018 (December) 21 (4) : 395 ~ 405 DOI No. 10.1007/s12892-018-0189-0 RESEARCH ARTICLE
Development of a Core Collection Based on EST-SSR Markers and Phenotypic Traits in Foxtail Millet [Setaria italica (L.) P. Beauv.] Yu-Mi Choi1, Kyung-Min Kim2, Sukyeung Lee1, Sejong Oh1, Myung-Chul Lee1* 1
National Agrobiodiversity Center, National Institute of Agricultural Science, RDA, 370 Nongsaengmyeong-ro, Deokjin-gu, Jeonju-si, Jeollabuk-do, 54874, Korea 2 School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Korea Received: October 10, 2018 / Revised: October 22, 2018 / Accepted: October 25, 2018 Ⓒ Korean Society of Crop Science and Springer 2018
Abstract The germplasm resources of foxtail millet reserve diverse genes for crop improvement which needs to be explored. To comprehend the maximum genetic diversity of this crop, a core collection with minimum number of accessions will facilitate easy access to genetic material. Here we assessed the genetic diversity and population structure in a large germplasm collection of 785 accessions by employing EST-SSR markers and morphological traits. A total of 107 alleles were detected with an average allele number of 4.9 per locus among the 785 accessions based on 22 EST-SSR markers. The number of alleles per locus ranged from 2 to 8. Polymorphism information content and expected heterozygosity ranged from 0.355 to 0.738 (mean = 0.525) and 0.451 to 0.771 (mean = 0.603), respectively. The germplasm collection was separated into three groups based on population structure analysis, whereas principal coordinate analysis (PCoA) could not cluster accessions according to their geographic origin. Subsequently, a core collection with a total of 170 accessions (21.66%) was selected from the whole set of germplasm by combining allelic variations of 22 EST-SSR markers and eight different phenotypic traits. The core collection optimally represented the whole germplasm collection and displayed a similar level of genetic diversity, population structure, and phenotypic variations based on various genetic analyses such as Shannon-Weaver and Nei’s diversity indices and PCoA, while phenotypic traits were analyzed by mean, range, and principal component analysis. This core collection of foxtail millet will be a primary resource for further genetic analysis and development of appropriate breeding strategies. Key words : Foxtail millet, core collection, genetic diversity, EST-SSR, population structure
Introduction Foxtail millet [Setaria italica (L.) P. Beauv. (2n = 18)] is one of the oldest crops and cultivated form of its wild ancestor S. viridis (green millet) (Li et al. 1945). It belongs to water efficient crops that grow rapidly under conditions of warm weather and dryness (Dekker 2003). It is still being grown in temperate regions of the world for fodder and grain food and plays a role in food security in many parts of Africa and Asia (Austin 2006). Foxtail millet became a minor crop in last 80 years due to rapid development in other crops and Myung-Chu
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